Fixbug:sample_id

tasks/NGScheckMates.wdl

@@ -11,13 +11,13 @@ task NGScheckMates {
 		set -e
 		nt=$(nproc)
 		export NCM_HOME=/opt/NGSCheckMate
-		python /opt/NGSCheckMate/ncm_fastq.py -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt -f -s 0.3
+		python /opt/NGSCheckMate/ncm_fastq.py -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt -f -s 0.1
     # rename
-    mv output_all.txt {sample_id}_output_all.txt
-    mv wd.txt {sample_id}_wd.txt
-    mv output_corr_matrix.txt {sample_id}_output_corr_matrix.txt
-    mv output_matched.txt {sample_id}_output_matched.txt
-    mv r_script.r {sample_id}_r_script.r
+    mv output_all.txt ${sample_id}_output_all.txt
+    mv wd.txt ${sample_id}_wd.txt
+    mv output_corr_matrix.txt ${sample_id}_output_corr_matrix.txt
+    mv output_matched.txt ${sample_id}_output_matched.txt
+    mv r_script.r ${sample_id}_r_script.r
 	>>>
 
 	runtime {
@@ -27,10 +27,10 @@ task NGScheckMates {
     	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File all_txt="{sample_id}_output_all.txt"
-		File ncm="{sample_id}_wd.txt"
-		File cor_txt="{sample_id}_output_corr_matrix.txt"
-		File matched_txt="{sample_id}_output_matched.txt"
-		File r_script="{sample_id}_r_script.r"
+		File all_txt="${sample_id}_output_all.txt"
+		File ncm="${sample_id}_wd.txt"
+		File cor_txt="${sample_id}_output_corr_matrix.txt"
+		File matched_txt="${sample_id}_output_matched.txt"
+		File r_script="${sample_id}_r_script.r"
 	}
 }